Hooo.... Too much lack-of-knowledge floating around in here...
First question:
Have you given your "fun" creatures any special names or easy-to-see abilities? It is impossible to tell the size of a creature just by looking at it.
Second question:
Are you editing files in data/objects or raw/objects? It sounds like you're editing the stuff in raw/objects, but I can't figure out why that wouldn't be working.
Third question:
Would you mind posting the code for one of your custom critters? This problem doesn't seem related to anything inside the creature code itself, but I's nice to cover all the bases.
It is perfectly possible to overwrite any and all vanilla animals. There is absolutely nothing hardcoded that creates creatures that fill "gaps". If there is a missing creature where there should be one (the only place where this would come up would be with the various entities), the game will simply enter into an infinite map-rejection loop. You do not need to delete the contents of data/objects unless you've made new text files that have different names from the originals.
Actually, I think I may have hit on the problem. Did you create new .txt files to hold your custom creatures? If so, are they named something different from the vanilla files?
If you created new files and deleted the old ones, the old ones would remain in data/objects since they wouldn't be overwritten next time the game loads from raw/objects. And if you forgot to put in the proper file headers in your new creature files, the game wouldn't be able to read the file and the creatures inside that file would not appear in-game.